This is bug 12144 (http://bugs.winehq.org/show_bug.cgi?id=12144).
You don't need winetricks for this. Instead set winver to Windows 2000 FOR THE INSTALLATION of Endnote. After the installation (with winver=win2000) the application launches with both settings: win2000 or winXP.
Probably the AppDB entry was a bit confusing, I tried to make it clearer now.
Please report your findings in the bug report mentioned above, as this is apparently not working for all systems.
Daniel